+Open data
-Basic information
Entry | Database: PDB / ID: 4ybq | ||||||
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Title | Rat GLUT5 with Fv in the outward-open form | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/IMMUNE SYSTEM / SUGAR TRANSPORTER / MAJOR FACILITATOR SUPERFAMILY / TRANSPORT PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information Intestinal hexose absorption / regulation of systemic arterial blood pressure mediated by a chemical signal / fructose transmembrane transporter activity / fructose import across plasma membrane / fructose transmembrane transport / fructose binding / glucose transmembrane transporter activity / glucose transmembrane transport / cellular response to fructose stimulus / response to fructose ...Intestinal hexose absorption / regulation of systemic arterial blood pressure mediated by a chemical signal / fructose transmembrane transporter activity / fructose import across plasma membrane / fructose transmembrane transport / fructose binding / glucose transmembrane transporter activity / glucose transmembrane transport / cellular response to fructose stimulus / response to fructose / Neutrophil degranulation / plasma membrane => GO:0005886 / sarcolemma / apical plasma membrane / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å | ||||||
Authors | Nomura, N. / Shimamura, T. / Iwata, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nature / Year: 2015 Title: Structure and mechanism of the mammalian fructose transporter GLUT5 Authors: Nomura, N. / Verdon, G. / Kang, H.J. / Shimamura, T. / Nomura, Y. / Sonoda, Y. / Hussien, S.A. / Qureshi, A.A. / Coincon, M. / Sato, Y. / Abe, H. / Nakada-Nakura, Y. / Hino, T. / Arakawa, T. ...Authors: Nomura, N. / Verdon, G. / Kang, H.J. / Shimamura, T. / Nomura, Y. / Sonoda, Y. / Hussien, S.A. / Qureshi, A.A. / Coincon, M. / Sato, Y. / Abe, H. / Nakada-Nakura, Y. / Hino, T. / Arakawa, T. / Kusano-Arai, O. / Iwanari, H. / Murata, T. / Kobayashi, T. / Hamakubo, T. / Kasahara, M. / Iwata, S. / Drew, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ybq.cif.gz | 558.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ybq.ent.gz | 467.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ybq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/4ybq ftp://data.pdbj.org/pub/pdb/validation_reports/yb/4ybq | HTTPS FTP |
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-Related structure data
Related structure data | 4yb9C 3o7qS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56425.801 Da / Num. of mol.: 2 / Mutation: N50Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc2a5, Glut5 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P43427 #2: Antibody | Mass: 13446.994 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Brevibacillus choshinensis (bacteria) #3: Antibody | Mass: 14863.454 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Brevibacillus choshinensis (bacteria) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 33-35% PEG400, 0.12 M CaCl2, 0.1 M Tris-HCl pH8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 22, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.27→50 Å / Num. obs: 38017 / % possible obs: 99.9 % / Redundancy: 13 % / Net I/σ(I): 1.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O7Q Resolution: 3.27→36.491 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.27→36.491 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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